R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

Pre-process both the pathology and the endoscopy text:

Merge endoscopy and pathology text

Clean the endoscopist and instrument columns

Extract number of biopsies, biopsy size, biopsy location and medications from the text

Extract endoscopy events

Extract some generic analyses

## Warning in eval_tidy(pair$lhs, env = default_env): NAs introduced by
## coercion

## Warning in eval_tidy(pair$lhs, env = default_env): NAs introduced by
## coercion

## Warning in eval_tidy(pair$lhs, env = default_env): NAs introduced by
## coercion

## Warning in eval_tidy(pair$lhs, env = default_env): NAs introduced by
## coercion

## Warning in eval_tidy(pair$lhs, env = default_env): NAs introduced by
## coercion

## Warning in eval_tidy(pair$lhs, env = default_env): NAs introduced by
## coercion

Extract some disease specific analyses

## Warning: `legend.margin` must be specified using `margin()`. For the old
## behavior use legend.spacing

Show the Consort diagram

Show the CodeDepends

## Loading required package: Rgraphviz
## Loading required package: graph
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind,
##     colMeans, colnames, colSums, dirname, do.call, duplicated,
##     eval, evalq, Filter, Find, get, grep, grepl, intersect,
##     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
##     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
##     Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
##     table, tapply, union, unique, unsplit, which, which.max,
##     which.min
## Loading required package: grid

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.